PDBsum entry: 1apw

Hydrolase/hydrolase inhibitor

PDB id: 1apw

Contents

Protein chain

323 a.a. *

Ligands

IVA-VAL-VAL-DFI-NME

MAN

HSY

SO4

DMF

Waters ×295

* Residue conservation analysis

PDB id:

1apw

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystallographic analysis of transition state mimics bound t penicillopepsin: difluorostatine-and difluorostatone-contai peptides

Structure:

Penicillopepsin. Chain: e. Engineered: yes. Inhibitor isovaleryl (iva)-val-val-difluorostatin methylamine. Chain: i. Engineered: yes. Other_details: transition state mimic

Source:

Penicillium janthinellum. Penicillium vitale. Organism_taxid: 5079.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.80Å R-factor: 0.131

Authors:

A.R.Sielecki,M.N.G.James

Key ref:

M.N.James et al. (1992). Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine- and difluorostatone-containing peptides. Biochemistry, 31, 3872-3886. PubMed id: 1567842 DOI: 10.1021/bi00130a019

Date:

16-Dec-91 Release date: 31-Jan-94

Protein chain

P00798  (PENP_PENJA) -  Penicillopepsin

Seq: 323 a.a.

Struc: 323 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.23.20 - Penicillopepsin.
• Reaction: Hydrolysis of proteins with broad specificity similar to that of pepsin A, preferring hydrophobic residues at P1 and P1', but also cleaving 20-Gly-|-Glu-21 in the B chain of insulin. Clots milk, and activates trypsinogen.

 Gene Ontology (GO) functional annotation 

• Biological process: proteolysis (1 term)
• Biochemical function: hydrolase activity (3 terms)

DOI no: 10.1021/bi00130a019

Biochemistry 31:3872-3886 (1992)

PubMed id: 1567842

Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine- and difluorostatone-containing peptides.

M.N.James, A.R.Sielecki, K.Hayakawa, M.H.Gelb.

ABSTRACT

Difluorostatine- and difluorostatone-containing peptides have been evaluated as potent inhibitors of penicillopepsin, a member of the aspartic proteinase family of enzymes. Isovaleryl-Val-Val-StaF2NHCH3 [StaF2 = (S)-4-amino-2,2-difluoro-(R)-3-hydroxy-6-methylheptanoic acid] and isovaleryl-Val-Val-StoF2NHCH3 [StoF2 = (S)-4-amino-2,2-difluoro-3-oxo-6-methylheptanoic acid] have measured Ki's of 10 x 10(-9) and 1 x 10(-9) M, respectively, with this fungal proteinase. The StoF2-containing peptide binds 32-fold more tightly to the enzyme than the analogous peptide containing the non-fluorinated statine ethyl ester. Each compound was cocrystallized with penicillopepsin, intensity data were collected to 1.8-A resolution, and the atomic coordinates were refined to an R factor [formula: see text] of 0.131 for both complexes. The inhibitors bind in the active site of penicillopepsin in much the same fashion as do other statine-containing inhibitors of penicillopepsin analyzed earlier [James, M. N. G., Sielecki, A. Salituro, F., Rich, D. H., & Hofmann, T. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6137-6141; James, M.N.G., Sielecki, A., & Hofmann, T. (1985) in Aspartic Proteinases and their Inhibitors (Kosta, V., Ed.) pp 163-177, Walter deGruyter, Berlin]. The (R)-3-hydroxyl group in StaF2 binds between the active site carboxyl groups of Asp33 and Asp213, making hydrogen-bonding contacts to each one. The ketone functional group of the StoF2 inhibitor is bound as a hydrated species, with the gem-diol situated between the two aspartic acid carboxyl groups in a manner similar to that predicted for the tetrahedral intermediate expected during the catalytic hydrolysis of a peptide bond [James, M. N. G., & Sielecki, A. (1985) Biochemistry 24, 3701-3713]. One hydrogen-bonding interaction from the "outer" hydroxyl group is made to O delta 1 of Asp33, and the "inner" hydroxyl group forms two hydrogen-bonding contacts, one to each of the carboxyl groups of Asp33 (O delta 2) and Asp213 (O delta 2). The only structural difference between the StaF2 and StoF2 inhibitors that accounts for the factor of 10 in their Ki's is the additional (R)-3-OH group on the tetrahedral sp3 carbon atom of the hydrated StoF2 inhibitor. The intermolecular interactions involving the fluorine atoms of each inhibitor are normal van der Waals contacts to one of the carboxyl oxygen atoms of Asp213 (F2-O delta 2 Asp213, 2.9 A). The observed stereochemistry of the bound StoF2 group in the active site of penicillopepsin has stimulated our reappraisal of the catalytic pathway for the aspartic proteinases.(ABSTRACT TRUNCATED AT 400 WORDS)